<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"> <style>
	.KEYW {color: #933;}
	.COMM {color: #bbb; font-style: italic;}
	.NUMB {color: #393;}
	.STRN {color: #393;}
	.REGX {color: #339;}
	.line {border-right: 1px dotted #666; color: #666; font-style: normal;}
	</style></head><body><pre><span class='line'>  1</span> <span class="COMM">/**
<span class='line'>  2</span> * @lends Bio.Seq
<span class='line'>  3</span> */</span><span class="WHIT">
<span class='line'>  4</span> </span><span class="NAME">Bio.Seq</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">Class.create</span><span class="PUNC">(</span><span class="NAME">Bio.Root</span><span class="PUNC">,</span><span class="PUNC">{</span><span class="WHIT"> 
<span class='line'>  5</span> </span><span class="COMM">/**
<span class='line'>  6</span>  * Bio.Seq
<span class='line'>  7</span>  * @Author Lee Katz &lt;lskatz@gmail.com>
<span class='line'>  8</span>  * @class An interface for Seq objects.
<span class='line'>  9</span>  * @constructs
<span class='line'> 10</span>  * @extends Bio.Root
<span class='line'> 11</span>  */</span><span class="WHIT">
<span class='line'> 12</span> </span><span class="WHIT">  </span><span class="NAME">initialize</span><span class="PUNC">:</span><span class="WHIT"> </span><span class="KEYW">function</span><span class="PUNC">(</span><span class="NAME">$super</span><span class="PUNC">,</span><span class="NAME">args</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 13</span> </span><span class="WHIT">    </span><span class="NAME">$super</span><span class="PUNC">(</span><span class="NAME">args</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 14</span> </span><span class="WHIT">    
<span class='line'> 15</span>     </span><span class="COMM">// default variables</span><span class="WHIT">
<span class='line'> 16</span> </span><span class="WHIT">    </span><span class="NAME">this.options</span><span class="WHIT"> </span><span class="PUNC">=</span><span class="WHIT"> </span><span class="NAME">Object.extend</span><span class="PUNC">(</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 17</span> </span><span class="WHIT">      </span><span class="NAME">id</span><span class="PUNC">:</span><span class="STRN">""</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 18</span> </span><span class="WHIT">      </span><span class="NAME">seq</span><span class="PUNC">:</span><span class="STRN">""</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 19</span> </span><span class="WHIT">      </span><span class="NAME">desc</span><span class="PUNC">:</span><span class="STRN">""</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 20</span> </span><span class="WHIT">      </span><span class="NAME">alphabet</span><span class="PUNC">:</span><span class="STRN">'dna'</span><span class="WHIT"> </span><span class="COMM">// TODO use a DNA class instead of a string</span><span class="WHIT">
<span class='line'> 21</span> </span><span class="WHIT">    </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT"> </span><span class="NAME">this.options</span><span class="PUNC">||</span><span class="WHIT"> </span><span class="PUNC">{</span><span class="WHIT"> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 22</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 23</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 24</span>    * The sequence
<span class='line'> 25</span>    * @returns String
<span class='line'> 26</span>    */</span><span class="WHIT">
<span class='line'> 27</span> </span><span class="WHIT">  </span><span class="NAME">seq</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 28</span> </span><span class="WHIT">    </span><span class="NAME">this.notImplemented</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 29</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 30</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 31</span>    * The ID of the sequence
<span class='line'> 32</span>    * @returns String
<span class='line'> 33</span>    */</span><span class="WHIT">
<span class='line'> 34</span> </span><span class="WHIT">  </span><span class="NAME">id</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 35</span> </span><span class="WHIT">    </span><span class="NAME">this.notImplemented</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 36</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 37</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 38</span>    * The description of the sequence, sans ID
<span class='line'> 39</span>    * @returns String
<span class='line'> 40</span>    */</span><span class="WHIT">
<span class='line'> 41</span> </span><span class="WHIT">  </span><span class="NAME">desc</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 42</span> </span><span class="WHIT">    </span><span class="NAME">this.notImplemented</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 43</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="PUNC">,</span><span class="WHIT">
<span class='line'> 44</span> </span><span class="WHIT">  </span><span class="COMM">/**
<span class='line'> 45</span>    * The alphabet of the sequence
<span class='line'> 46</span>    * @returns Alphabet
<span class='line'> 47</span>    */</span><span class="WHIT">
<span class='line'> 48</span> </span><span class="WHIT">  </span><span class="NAME">alphabet</span><span class="PUNC">:</span><span class="KEYW">function</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">{</span><span class="WHIT">
<span class='line'> 49</span> </span><span class="WHIT">    </span><span class="NAME">this.notImplemented</span><span class="PUNC">(</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 50</span> </span><span class="WHIT">  </span><span class="PUNC">}</span><span class="WHIT">
<span class='line'> 51</span> </span><span class="PUNC">}</span><span class="PUNC">)</span><span class="PUNC">;</span><span class="WHIT">
<span class='line'> 52</span> </span></pre></body></html>